From: Chris Harrison (charris5_at_nd.edu)
Date: Sun Jan 04 2009 - 12:12:07 CST
Look at the programs CURVES or X3DNA, they may be of assistance; however I
don't think they have a "occupancy" definition, or that they handle RNA (in
addition to DNA).
Why not take a similar approach to that in DNA and for a give secondary
structure of RNA define optimal base stacking (as indicated via a local
energy minimum of a PMF where the reaction coordinate is the twisting of the
base out of the "stack") as occupancy 1 and completely orthogonal bases as
occupancy 0, with a range in between labeled for 0.1, 0.2, etc.
-- Chris Harrison, Ph.D. Theoretical and Computational Biophysics Group NIH Resource for Macromolecular Modeling and Bioinformatics Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801 char_at_ks.uiuc.edu Voice: 217-244-1733 http://www.ks.uiuc.edu/~char Fax: 217-244-6078 On Tue, Dec 30, 2008 at 3:54 PM, Tianjiao Wang <tjwang_at_iastate.edu> wrote: > Dear all, > > I have finished a molecular dynamics simulation of a small RNA by NAMD > 2.6. > I am wondering whether there is a way to quantify the occupancy of base > stackings between residues from the MD trajectory. Thank you very much for > your advice and happy holiday! > > Tianjiao > > Tianjiao Wang > 3288 MBB > Iowa State Univ > Ames, IA 50010 > e-mail: tjwang_at_iastate.edu > > > > > > > > > > > > >
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